Hi FreeSurfer users,
I've tried the following from my $SUBJECT_DIR/SubjectX/mri directory:
mri_label2vol --seg aseg.mgz --regheader rawavg.mgz --o aseg-in-rawavg.mgz --temp aseg.mgz
I have the following error in return:
ERROR: Option --regheader unknown
Any ideas where does it comes?
Thanks a lot, Have a good day, Delphine
________________________________________ De : Douglas N Greve [greve@nmr.mgh.harvard.edu] Date d'envoi : mardi 3 novembre 2009 18:48 À : Ribes Delphine Cc : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] RE : RE : Skull Stripping Free surfer
Check out this page and see if it answers your questions
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Ribes Delphine wrote:
Hi,
I've tested to use directly mri_watershed but then you have to set the seeds for watershed initiaization.
The idea is to create an automatic pipeline (as I have a bunch of data to process) and get the results into the subject space coordinate.
In subjects directories, I've seen one called transform. Inside this directory, there is some file with (I suppose) the affine transform applied. Is there a freeSurfer command to do the inverse transform? Also there is a "conformalization" to put all volume in 256 cube with 1mm cube spacing. Is there a command in FreeSurfer to get back the original volume?
After the inverse affine transform and the inverse conformalization, I will have (hopefully), my skullstrip volume into his original space coordinate?
Thanks Delphine
De : Bruce Fischl [fischl@nmr.mgh.harvard.edu] Date d'envoi : mardi 3 novembre 2009 15:09 À : Ribes Delphine Cc : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] RE : Skull Stripping Free surfer
yes, it's possible. You'll need to download and install freesurfer, then try out the mri_watershed command (or just run recon-all on your data, mri_watershed is one of the steps it runs) On Tue, 3 Nov 2009, Ribes Delphine wrote:
Hi,
Looking at Literature, HWA algorithm seems to perform well for my kind of data. Also the results I've got seems to confirm this hypothesis. But if possible I would like to siwcth of the affine registration.
So yes I would like only to do skull strip using HWA algorithm. Is it possible to do so in freesurfer? :-)
Thanks
De : Pedro Paulo de Magalhães Oliveira Junior [ppj@netfilter.com.br] Date d'envoi : mardi 3 novembre 2009 13:43 À : Ribes Delphine Cc : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Skull Stripping Free surfer
Using FreeSurfer just for Skull Striping is like killing an ant with an MP5 :)
Are you sure you just want to skull strip?
2009/11/3 Ribes Delphine <delphine.ribes@epfl.chmailto:delphine.ribes@epfl.ch> Dear Users,
I've just started using FreeSurfer. I would like to use it for skull-stripping.
I've created a batch file to process all my subjects. and I am basically using the command line:
recon-all -autorecon1 -skullstrip -s subj1
I would like to know if there is a way to only do skull-stripping and not doing the Talairach Transform and then INU correction?
I would like to have the skulll-stripp volume in the same space coordinate as originally?
Otherwise, I am doing skull-stripping of T1 weighted images of normal elderly subejcts. Is there any specific recommandation for skull-stripping parameters?
Thanks a lot, Delphine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I think you may have a slightly older version of mri_label2vol. Try creating a register.dat with tkregister2 using the --regheader option, then pass that to mri_vol2vol.
doug
Ribes Delphine wrote:
Hi FreeSurfer users,
I've tried the following from my $SUBJECT_DIR/SubjectX/mri directory:
mri_label2vol --seg aseg.mgz --regheader rawavg.mgz --o aseg-in-rawavg.mgz --temp aseg.mgz
I have the following error in return:
ERROR: Option --regheader unknown
Any ideas where does it comes?
Thanks a lot, Have a good day, Delphine
De : Douglas N Greve [greve@nmr.mgh.harvard.edu] Date d'envoi : mardi 3 novembre 2009 18:48 À : Ribes Delphine Cc : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] RE : RE : Skull Stripping Free surfer
Check out this page and see if it answers your questions
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Ribes Delphine wrote:
Hi,
I've tested to use directly mri_watershed but then you have to set the seeds for watershed initiaization.
The idea is to create an automatic pipeline (as I have a bunch of data to process) and get the results into the subject space coordinate.
In subjects directories, I've seen one called transform. Inside this directory, there is some file with (I suppose) the affine transform applied. Is there a freeSurfer command to do the inverse transform? Also there is a "conformalization" to put all volume in 256 cube with 1mm cube spacing. Is there a command in FreeSurfer to get back the original volume?
After the inverse affine transform and the inverse conformalization, I will have (hopefully), my skullstrip volume into his original space coordinate?
Thanks Delphine
De : Bruce Fischl [fischl@nmr.mgh.harvard.edu] Date d'envoi : mardi 3 novembre 2009 15:09 À : Ribes Delphine Cc : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] RE : Skull Stripping Free surfer
yes, it's possible. You'll need to download and install freesurfer, then try out the mri_watershed command (or just run recon-all on your data, mri_watershed is one of the steps it runs) On Tue, 3 Nov 2009, Ribes Delphine wrote:
Hi,
Looking at Literature, HWA algorithm seems to perform well for my kind of data. Also the results I've got seems to confirm this hypothesis. But if possible I would like to siwcth of the affine registration.
So yes I would like only to do skull strip using HWA algorithm. Is it possible to do so in freesurfer? :-)
Thanks
De : Pedro Paulo de Magalhães Oliveira Junior [ppj@netfilter.com.br] Date d'envoi : mardi 3 novembre 2009 13:43 À : Ribes Delphine Cc : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Skull Stripping Free surfer
Using FreeSurfer just for Skull Striping is like killing an ant with an MP5 :)
Are you sure you just want to skull strip?
2009/11/3 Ribes Delphine <delphine.ribes@epfl.chmailto:delphine.ribes@epfl.ch> Dear Users,
I've just started using FreeSurfer. I would like to use it for skull-stripping.
I've created a batch file to process all my subjects. and I am basically using the command line:
recon-all -autorecon1 -skullstrip -s subj1
I would like to know if there is a way to only do skull-stripping and not doing the Talairach Transform and then INU correction?
I would like to have the skulll-stripp volume in the same space coordinate as originally?
Otherwise, I am doing skull-stripping of T1 weighted images of normal elderly subejcts. Is there any specific recommandation for skull-stripping parameters?
Thanks a lot, Delphine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Ribes Delphine